CollessLike specifications

Information


Unique identifier OMICS_28399
Name CollessLike
Alternative name total cophenetic index
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
igraph, ape, R(≥3.3.0)
Source code URL https://cran.r-project.org/src/contrib/CollessLike_1.0.tar.gz
Maintained Yes

Download


download.png

Versioning


No version available

Documentation


Maintainers


  • person_outline Arnau Mir
  • person_outline Francesc Rossello
  • person_outline Lucia Rotger

Additional information


https://github.com/LuciaRotger/CollessLike

Publication for CollessLike

CollessLike citations

 (2)
library_books

Unbiased Taxonomic Annotation of Metagenomic Samples

2018
J Comput Biol
PMCID: 5865273
PMID: 29028181
DOI: 10.1089/cmb.2017.0144

[…] binary reference taxonomy is a rooted caterpillar, as every internal node (and also the root) has one big descendant clade and one small (with only one node) descendant clade. Borrowing the notion of total cophenetic index for phylogenetic trees (Mir et al., ) to measure the balance of reference taxonomies, complete binary trees have indeed the minimum value while rooted caterpillars have the maxi […]

library_books

Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps

2017
Sci Rep
PMCID: 5460120
PMID: 28588246
DOI: 10.1038/s41598-017-03107-y

[…] tochondrial genes (PCGs). Nucleotide substitution saturation was assessed using the Xia’s test. The balance of the phylogenetic tree obtained under the best partitioning scheme was measured using the total cophenetic index. PartitionFinder was used to explore the partitioning schemes and evolutionary models for the standard DNA-based and the protein-based analyses. Tree topologies were analysed us […]

CollessLike institution(s)
Research Institute of Health Science (IUNICS) and Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, Spain; Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, Spain
CollessLike funding source(s)
Supported by the Spanish government and the UE FEDER program, through projects MTM2009-07165 and TIN2011-15874-E.

CollessLike reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CollessLike